Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:25 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the RnBeads package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RnBeads.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1698/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RnBeads 2.17.0 (landing page) Fabian Mueller
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: RnBeads |
Version: 2.17.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings RnBeads_2.17.0.tar.gz |
StartedAt: 2023-02-07 13:45:39 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 13:57:57 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 738.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: RnBeads.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings RnBeads_2.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/RnBeads.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘RnBeads/DESCRIPTION’ ... OK * this is package ‘RnBeads’ version ‘2.17.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'GenomicRanges', 'MASS', 'cluster', 'ff', 'fields', 'ggplot2', 'gplots', 'grid', 'gridExtra', 'limma', 'matrixStats', 'illuminaio', 'methylumi', 'plyr' Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘RnBeads’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.5Mb sub-directories of 1Mb or more: R 3.1Mb bin 1.0Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘qvalue’ A package should be listed in only one of these fields. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... NOTE Warning: no function found corresponding to methods exports from ‘RnBeads’ for: ‘samples’ A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Killed * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Killed * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘RnBeads-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: rnb.execute.pOOBAH > ### Title: rnb.execute.pOOBAH > ### Aliases: rnb.execute.pOOBAH > > ### ** Examples > > library(RnBeads.hg19) > data(small.example.object) > filtered <- rnb.execute.pOOBAH(rnb.set.example) Killed * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ ERROR Running the tests in ‘tests/runTests.R’ failed. Last 13 lines of output: 2023-02-07 13:54:58 1.4 STATUS STARTED Computing Differential Methylation Table 2023-02-07 13:54:58 1.4 INFO Conducting differential analysis using limma 2023-02-07 13:54:58 1.4 STATUS COMPLETED Computing Differential Methylation Table 2023-02-07 13:54:58 1.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2023-02-07 13:55:00 1.4 STATUS Computed table for tiling 2023-02-07 13:55:00 1.4 STATUS Computed table for genes 2023-02-07 13:55:00 1.4 STATUS Computed table for promoters 2023-02-07 13:55:00 1.4 STATUS Computed table for cpgislands 2023-02-07 13:55:00 1.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2023-02-07 13:55:00 1.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2023-02-07 13:55:00 1.4 STATUS COMPLETED Computing differential methylation tables 2023-02-07 13:55:00 1.4 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth 2023-02-07 13:55:00 1.4 STATUS STARTED Testing function: diffVar 2023-02-07 13:55:01 1.4 STATUS STARTED diffVar method Killed * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘RnBeads.Rnw’... failed to complete the test ‘RnBeads_Annotations.Rnw’... OK ERROR Errors in running code in vignettes: when running code in ‘RnBeads.Rnw’ ... 8 hiPS_17b_p35_TeSR hiPS_17b TRUE 9 hiPS_27b_p31 hiPS_27b TRUE 10 hES_HUES64_p19 hES_HUES64 FALSE 11 hiPS_17b_p35_KOSR hiPS_17b TRUE 12 hES_H9_p58 hES_H9 FALSE > Mint <- M(rnb.set.example, row.names = TRUE) Killed ... incomplete output. Crash? * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 ERRORs, 7 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/RnBeads.Rcheck/00check.log’ for details.
RnBeads.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL RnBeads ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘RnBeads’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RnBeads)
RnBeads.Rcheck/tests/runTests.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > BiocGenerics:::testPackage("RnBeads") Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'bit' The following object is masked from 'package:base': xor Attaching package ff - getOption("fftempdir")=="/tmp/RtmpgXZSnO/ff" - getOption("ffextension")=="ff" - getOption("ffdrop")==TRUE - getOption("fffinonexit")==TRUE - getOption("ffpagesize")==65536 - getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes - getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system - getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system Attaching package: 'ff' The following objects are masked from 'package:utils': write.csv, write.csv2 The following objects are masked from 'package:base': is.factor, is.ordered Spam version 2.9-1 (2022-08-07) is loaded. Type 'help( Spam)' or 'demo( spam)' for a short introduction and overview of this package. Help for individual functions is also obtained by adding the suffix '.spam' to the function name, e.g. 'help( chol.spam)'. Attaching package: 'spam' The following object is masked from 'package:stats4': mle The following objects are masked from 'package:base': backsolve, forwardsolve Try help(fields) to get started. Attaching package: 'gplots' The following object is masked from 'package:IRanges': space The following object is masked from 'package:S4Vectors': space The following object is masked from 'package:stats': lowess Attaching package: 'grid' The following object is masked from 'package:ff': pattern Attaching package: 'gridExtra' The following object is masked from 'package:BiocGenerics': combine Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Attaching package: 'scales' The following object is masked from 'package:viridis': viridis_pal Attaching package: 'AnnotationDbi' The following object is masked from 'package:MASS': select Attaching package: 'MatrixGenerics' The following object is masked from 'package:Biobase': rowMedians The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Attaching package: 'Biostrings' The following object is masked from 'package:grid': pattern The following objects are masked from 'package:ff': mismatch, pattern The following object is masked from 'package:base': strsplit locfit 1.5-9.7 2023-01-02 Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) Attaching package: 'plyr' The following object is masked from 'package:XVector': compact The following object is masked from 'package:matrixStats': count The following object is masked from 'package:IRanges': desc The following object is masked from 'package:S4Vectors': rename 2023-02-07 13:54:51 1.1 STATUS STARTED Unit testing: differential 2023-02-07 13:54:51 1.1 STATUS STARTED Testing function: rowWelchP Loading required package: RnBeads.hg19 2023-02-07 13:54:51 1.1 STATUS COMPLETED Testing function: rowWelchP 2023-02-07 13:54:51 1.1 STATUS STARTED Testing function: limmaP 2023-02-07 13:54:51 1.1 STATUS COMPLETED Testing function: limmaP 2023-02-07 13:54:51 1.1 STATUS STARTED Testing function: computeDiffTab.extended.site 2023-02-07 13:54:51 1.1 INFO Conducting differential analysis using limma 2023-02-07 13:54:51 1.1 STATUS COMPLETED Testing function: computeDiffTab.extended.site 2023-02-07 13:54:51 1.1 STATUS STARTED Testing function: computeDiffTab.default.region 2023-02-07 13:54:52 1.1 INFO Conducting differential analysis using limma 2023-02-07 13:54:56 1.2 STATUS COMPLETED Testing function: computeDiffTab.default.region 2023-02-07 13:54:56 1.2 STATUS STARTED Testing function: combineTestPvalsMeth 2023-02-07 13:54:56 1.2 STATUS COMPLETED Testing function: combineTestPvalsMeth 2023-02-07 13:54:56 1.2 STATUS STARTED Testing function: get.adjustment.variables 2023-02-07 13:54:56 1.2 STATUS COMPLETED Testing function: get.adjustment.variables 2023-02-07 13:54:56 1.2 STATUS STARTED Testing function: get.comparison.info 2023-02-07 13:54:56 1.2 STATUS COMPLETED Testing function: get.comparison.info 2023-02-07 13:54:56 1.2 STATUS STARTED Testing function: rnb.execute.computeDiffMeth 2023-02-07 13:54:56 1.2 STATUS STARTED Retrieving comparison info 2023-02-07 13:54:56 1.2 STATUS COMPLETED Retrieving comparison info 2023-02-07 13:54:56 1.2 STATUS STARTED Computing differential methylation tables 2023-02-07 13:54:56 1.2 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2023-02-07 13:54:56 1.2 STATUS STARTED Computing Differential Methylation Table 2023-02-07 13:54:56 1.2 INFO Conducting differential analysis using limma 2023-02-07 13:54:56 1.2 STATUS COMPLETED Computing Differential Methylation Table 2023-02-07 13:54:56 1.2 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2023-02-07 13:54:57 1.3 STATUS Computed table for tiling 2023-02-07 13:54:57 1.4 STATUS Computed table for genes 2023-02-07 13:54:57 1.4 STATUS Computed table for promoters 2023-02-07 13:54:58 1.4 STATUS Computed table for cpgislands 2023-02-07 13:54:58 1.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2023-02-07 13:54:58 1.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2023-02-07 13:54:58 1.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2023-02-07 13:54:58 1.4 STATUS STARTED Computing Differential Methylation Table 2023-02-07 13:54:58 1.4 INFO Conducting differential analysis using limma 2023-02-07 13:54:58 1.4 STATUS COMPLETED Computing Differential Methylation Table 2023-02-07 13:54:58 1.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2023-02-07 13:55:00 1.4 STATUS Computed table for tiling 2023-02-07 13:55:00 1.4 STATUS Computed table for genes 2023-02-07 13:55:00 1.4 STATUS Computed table for promoters 2023-02-07 13:55:00 1.4 STATUS Computed table for cpgislands 2023-02-07 13:55:00 1.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2023-02-07 13:55:00 1.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2023-02-07 13:55:00 1.4 STATUS COMPLETED Computing differential methylation tables 2023-02-07 13:55:00 1.4 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth 2023-02-07 13:55:00 1.4 STATUS STARTED Testing function: diffVar 2023-02-07 13:55:01 1.4 STATUS STARTED diffVar method Killed
RnBeads.Rcheck/RnBeads-Ex.timings
name | user | system | elapsed | |
M-methods | 0 | 0 | 0 | |
U-methods | 0.000 | 0.000 | 0.001 | |
addDiffMethTable-RnBDiffMeth-methods | 0 | 0 | 0 | |
addPheno-RnBSet-methods | 0 | 0 | 0 | |
addRegionSubsegments | 0 | 0 | 0 | |
annotation-methods | 0 | 0 | 0 | |
assembly-methods | 0 | 0 | 0 | |
combine.rnb.sets-methods | 0 | 0 | 0 | |
combineTestPvalsMeth | 0.000 | 0.000 | 0.001 | |
computeDiffTab.region | 0 | 0 | 0 | |
computeDiffTab.site | 0 | 0 | 0 | |
covg-methods | 0 | 0 | 0 | |
create.densityScatter | 0 | 0 | 0 | |
create.scatter.dens.points | 0 | 0 | 0 | |
createReport | 0 | 0 | 0 | |
createReportPlot | 0 | 0 | 0 | |
downloadLolaDbs | 0 | 0 | 0 | |
dpval-methods | 0 | 0 | 0 | |
exportDMRs2regionFile | 0 | 0 | 0 | |
get.adjustment.variables | 0 | 0 | 0 | |
get.comparison.grouplabels-RnBDiffMeth-methods | 0 | 0 | 0 | |
get.comparison.groupsizes-RnBDiffMeth-methods | 0.000 | 0.000 | 0.001 | |
get.comparison.info | 0 | 0 | 0 | |
get.comparisons-RnBDiffMeth-methods | 0 | 0 | 0 | |
get.covariates.sva | 0.000 | 0.000 | 0.001 | |
get.covg.thres-RnBDiffMeth-methods | 0 | 0 | 0 | |
get.files | 0 | 0 | 0 | |
get.region.types-RnBDiffMeth-methods | 0 | 0 | 0 | |
get.site.test.method-RnBDiffMeth-methods | 0 | 0 | 0 | |
get.table-RnBDiffMeth-methods | 0 | 0 | 0 | |
getCellTypesFromLolaDb | 0 | 0 | 0 | |
getNamesFromLolaDb | 0 | 0 | 0 | |
getSubCmdTokens-ClusterArchitectureSGE-methods | 0 | 0 | 0 | |
getSubCmdTokens-ClusterArchitectureSLURM-methods | 0 | 0 | 0 | |
getTargetFromLolaDb | 0 | 0 | 0 | |
has.covariates.sva | 0 | 0 | 0 | |
hasCovg-methods | 0 | 0 | 0 | |
includes.sites-RnBDiffMeth-methods | 0.000 | 0.000 | 0.001 | |
is.valid-RnBDiffMeth-methods | 0 | 0 | 0 | |
join.diffMeth-methods | 0 | 0 | 0 | |
limmaP | 0 | 0 | 0 | |
loadLolaDbs | 0 | 0 | 0 | |
logger.argument | 0 | 0 | 0 | |
logger.getfiles | 0 | 0 | 0 | |
logger.isinitialized | 0 | 0 | 0 | |
logger.validate.file | 0 | 0 | 0 | |
loggerManagement | 0 | 0 | 0 | |
loggerMessages | 0 | 0 | 0 | |
lolaBarPlot | 0 | 0 | 0 | |
lolaBoxPlotPerTarget | 0 | 0 | 0 | |
lolaVolcanoPlot | 0 | 0 | 0 | |
mergeSamples-methods | 0 | 0 | 0 | |
meth-methods | 0 | 0 | 0 | |
mval-methods | 0 | 0 | 0 | |
nsites-methods | 0 | 0 | 0 | |
parallel.getNumWorkers | 0 | 0 | 0 | |
parallel.isEnabled | 0 | 0 | 0 | |
parallel.setup | 0 | 0 | 0 | |
parallel.teardown | 0 | 0 | 0 | |
performGOEnrichment.diffVar | 0 | 0 | 0 | |
performGOenrichment.diffMeth.entrez | 0 | 0 | 0 | |
performGoEnrichment.diffMeth | 0 | 0 | 0 | |
performLolaEnrichment.diffMeth | 0 | 0 | 0 | |
performLolaEnrichment.diffVar | 0 | 0 | 0 | |
pheno-methods | 0 | 0 | 0 | |
qc-methods | 0 | 0 | 0 | |
read.sample.annotation | 0 | 0 | 0 | |
regionMapping-methods | 0 | 0 | 0 | |
regions-methods | 0 | 0 | 0 | |
reload-RnBDiffMeth-methods | 0 | 0 | 0 | |
remove.regions-methods | 0 | 0 | 0 | |
remove.samples-methods | 0 | 0 | 0 | |
remove.sites-methods | 0 | 0 | 0 | |
rnb.RnBSet.to.GRangesList | 0 | 0 | 0 | |
rnb.RnBSet.to.bed | 0 | 0 | 0 | |
rnb.RnBSet.to.bedGraph | 0 | 0 | 0 | |
rnb.add.list | 0 | 0 | 0 | |
rnb.add.paragraph | 0 | 0 | 0 | |
rnb.add.reference | 0 | 0 | 0 | |
rnb.add.section | 0 | 0 | 0 | |
rnb.annotation.size | 0 | 0 | 0 | |
rnb.annotation2data.frame | 0 | 0 | 0 | |
rnb.beta2mval | 0 | 0 | 0 | |
rnb.execute.batcheffects | 0 | 0 | 0 | |
rnb.execute.clustering | 0 | 0 | 0 | |
rnb.execute.computeDiffMeth | 0 | 0 | 0 | |
rnb.execute.context.removal | 0 | 0 | 0 | |
rnb.execute.cross.reactive.removal | 0 | 0 | 0 | |
rnb.execute.dreduction | 0 | 0 | 0 | |
rnb.execute.export.csv | 0 | 0 | 0 | |
rnb.execute.greedycut | 0 | 0 | 0 | |
rnb.execute.import | 0 | 0 | 0 | |
rnb.execute.na.removal | 0 | 0 | 0 | |
rnb.execute.normalization | 0 | 0 | 0 | |